3QKA | pdb_00003qka

Crystal structure of enoyl-CoA hydratase EchA5 from Mycobacterium marinum

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3H81	PDB ENTRY 3H81

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	289	Crystal tracking ID 218457h19. JCSG+ screen condition H10: 0.2 M ammonium acetate, 0.1 M Bis-Tris propane, 25% PEG3350, 46.3 mg/mL MymaA.00386.a.A1 PS00820, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.04	α = 90
b = 118.92	β = 90
c = 132.48	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RIGAKU SATURN 944+	VariMax	2011-01-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.15	50	97.4	0.092	11.08	4	75404	73428		-3	31.017

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.21	90.7		0.461	2.44	2.6	5531

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3H81	2.15	50	73236	3698	97.13	0.1706	0.1683	0.18	0.2134	0.22	RANDOM	24.4438

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-1.34			0.71		0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.912
r_dihedral_angle_4_deg	18.456
r_dihedral_angle_3_deg	12.948
r_dihedral_angle_1_deg	5.868
r_scangle_it	3.299
r_scbond_it	2.106
r_angle_refined_deg	1.411
r_mcangle_it	1.148
r_mcbond_it	0.63
r_chiral_restr	0.091
r_bond_refined_d	0.015
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10339
Nucleic Acid Atoms
Solvent Atoms	672
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction